Changes

; Local Realignment Filter

; Local Realignment Filter

: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that a length polymorphism is present in the population.

: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that an [[indel]] polymorphism is present in the population.

; Read Depth

; Read Depth

: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.  

: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.

= Special Considerations for Admixed Samples =

= Special Considerations for Admixed Samples =